Table 5.
Summary of SNP reliability across species, sections and subgenera of Eucalyptus as measured by the number of SNP meeting the thresholds of call rate and GeneCall50 for two groups of SNPs that differed regarding the flanking sequence constraints during in silico SNP mining and GGGT assay design
| SNPs selected with no flanking sequence requirements (N = 372) |
SNPs selected with no additional SNPs in flanking sequence (N = 396) |
||||||||
|---|---|---|---|---|---|---|---|---|---|
| Subgenera/Section | Species | # SNPs with Call rate |
% SNPs with Call rate |
# SNPs with GC50 |
% SNPs with GC50 |
# SNPs with Call rate |
% SNPs with Call rate |
# SNPs with GC50 |
% SNPs with GC50 |
| ≥ 95% | ≥ 95% | ≥ 0.40 | ≥ 0.40 | ≥ 95% | ≥ 95% | ≥ 0.40 | ≥ 0.40 | ||
| Symphyomyrtus/Latoangulatae | E. grandis | 323 | 86.8 | 333 | 89.5 | 378 | 95.5 | 378 | 95.5 |
| Symphyomyrtus/Latoangulatae | E. urophylla | 310 | 83.3 | 335 | 90.1 | 369 | 93.2 | 377 | 95.2 |
| Symphyomyrtus/Latoangulatae | E. saligna | 279 | 75.0 | 328 | 88.2 | 343 | 86.6 | 376 | 94.9 |
| Symphyomyrtus/Maidenaria | E. globulus | 325 | 87.4 | 331 | 89.0 | 369 | 93.2 | 374 | 94.4 |
| Symphyomyrtus/Maidenaria | E. nitens | 311 | 83.6 | 327 | 87.9 | 369 | 93.2 | 375 | 94.7 |
| Symphyomyrtus/Maidenaria | E. dunnii | 295 | 79.3 | 324 | 87.1 | 361 | 91.2 | 371 | 93.7 |
| Symphyomyrtus/Maidenaria | E. viminalis | 300 | 80.6 | 325 | 87.4 | 353 | 89.1 | 370 | 93.4 |
| Symphyomyrtus/Exsertaria | E. camaldulensis | 289 | 77.7 | 336 | 90.3 | 339 | 85.6 | 376 | 94.9 |
| Symphyomyrtus/Exsertaria | E. tereticornis | 281 | 75.5 | 319 | 85.8 | 330 | 83.3 | 365 | 92.2 |
| Eucalyptus/Pseudophloius | E. pilularis | 194 | 52.2 | 271 | 72.8 | 246 | 62.1 | 325 | 82.1 |
| Idiogenes/Gympiaria | E. cloeziana | 166 | 44.6 | 223 | 59.9 | 198 | 50.0 | 278 | 70.2 |